seatrac_hackday_2024_code

Author

Madison Cox

Setup

filter out rare genes and normalize for CD8 and CD4 samples separately

For each dataset, I removed genes with expression in < 20% of samples and with < 10 CPM across samples

CD4 before-and-after removing rare genes

CD8 before-and-after removing rare genes

Voom normalization

CD4

CD8

Model logCFU vs gene

Just CD4_gran samples, association with logCFU

variable fdr<0.05 fdr<0.1 fdr<0.2 fdr<0.3 fdr<0.4 fdr<0.5
(1 | subject) 744 936 1245 1492 1785 1992
logCFU 35 85 482 1658 2720 3997
total (nonredundant) 779 1015 1692 2988 4167 5430

Just CD4_gran samples, association with logCFU

variable fdr<0.05 fdr<0.1 fdr<0.2 fdr<0.3 fdr<0.4 fdr<0.5
(1 | subject) 861 1202 1663 2106 2459 2850
logCFU 25 47 127 219 312 489
total (nonredundant) 886 1245 1780 2300 2730 3254

get top hits for low CFU-associated genes in CD4 and CD8

Just CD4_gran samples, genes with negative association with logCFU

$BFSP2


$LOC106998813


$LOC107001007


$LOC697141


$LOC698130


$LOC700872


$LOC702620


$LOC703283


$LOC706087


$LOC708140


$LOC709459


$LOC710859


$LOC712614


$LOC719289


$PSMD9


$SMIM12


$STOX1

Just CD8_gran samples, genes with negative association with logCFU

$ARHGAP19


$BTBD19


$C1H1orf198


$C7H14orf79


$C7H15orf62


$C9H10orf128


$C9H10orf90


$CFAP73


$ENKD1


$ENO3


$HEATR1


$KBTBD8


$LOC100429401


$LOC106997346


$LOC106998746


$LOC707027


$LOC720294


$PDCD1LG2


$RAD54L


$SFXN5


$SLC7A1


$STX3

look for agreement with Bromley

Sig negative corr in any cluster of Bromley, CD4_gran cells in Foreman (FDR < 0.2)

P-values represent interaction between group and logCFU on gene expression

$STOX1

Sig negative corr in any cluster of Bromley, CD8_gran cells in Foreman (FDR < 0.2)

P-values represent interaction between group and logCFU on gene expression

$STX3


$PDCD1LG2


$SLC7A1


$BTBD19


$HEATR1


$ENKD1


$C9H10orf128


$C1H1orf198


$SFXN5


$RAD54L


$ENO3


$C7H15orf62


$C7H14orf79


$ARHGAP19


$CFAP73